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Fluidigm Expects New Juno System to Help it Compete with Illumina, LGC, Agena in SNP Genotyping


NEW YORK (GenomeWeb) – Fluidigm is counting on a new sample preparation instrument to expand its share of the market for high-throughput SNP genotyping platforms.

The South San Francisco, Calif-based company last week announced an early access program for the system, dubbed Juno, which incorporates preamplification and genotyping in one of Fluidigm's integrated fluidic circuits, or IFCs.

According to the firm, Juno allows scientists to genotype low-concentration DNA samples from tissue, buccal swabs, formalin-fixed, paraffin-embedded samples, and polyploid organisms in less than three hours.

"With the integrated preamplification, the Juno System can also address key sample types that were previously impossible to use in high-throughput genotyping situations," spokesperson Howard High told BioArray News in an email this week.

"Applications in areas such as clinical and [sample identification] where tissue biopsies, FFPE, and buccal swabs are common, or in agbio where polyploid and crude samples are used, will benefit from this capability and are places that we believe will benefit from the Juno System," he said.

High noted that Fluidigm will fully commercialize Juno in the first quarter of 2015.

While Juno does all of the sample preparation through thermal cycling, High noted that Fluidigm must transfer the IFCs to one of its BioMark or EP1 genotyping systems to obtain real-time or end-point reads.

Still, the company sees the new system as an additional incentive to adopt its genotyping platforms over others on the market. High specifically named Illumina's BeadXpress and GoldenGate Genotyping BeadArrays, LGC Genomics' KASP assay, Agena Bioscience's MassArray, and Thermo Fisher Scientific's QuantStudio/OpenArray as platforms with which Fluidigm competes directly.

Juno consists of an instrument that controls and thermal cycles its IFCs as well as a new IFC with optimized reagents and master mixes that enable genotyping from extremely low DNA input amounts. The system also handles all control and cycling of existing Fluidigm genotyping IFCs including its 48 -by-48, 96 -by-96, and 192- 24 assay formats, High said.

Following preparation with Juno, customers can run both probe-based genotyping Taqman assays as well as Fluidigm's SNPtype competitive allele-specific PCR assays, giving them the flexibility to run the assays they have already validated, High noted. Fluidigm is also releasing new master mix chemistries that combine all of the reagents needed to perform integrated genotyping for both probe-based chemistry and SNPtype chemistry, he said.

Another perceived benefit is the system's low sample input requirements. High said that the system requires as little as 5.5 nanograms of DNA with a concentration of 2.5 nanograms per microliter, while competing platforms, such as Thermo Fisher Scientific's QuantStudio 12K Flex Real-Time PCR System, require 50 nanograms of DNA. High also said that competing systems such as Agena's MassArray have a turnaround time of up to six hours versus 2.5 hours for Juno.

Fluidigm also sees the fact that sample preparation takes place within its closed IFCs as a means to "diminish the risks of error and PCR contamination inherent in multi-step protocols conducted in open-air microtiter plates," High said.

He declined to speculate on future revenue contributions from the launch of the system.

Diverse applications

It has taken Fluidigm years to develop Juno. In 2009, company representatives discussed the development of a "sample processor chip" with the aim to get it on the market by 2011.

"One of biggest hurdles was fitting the preamplification into the same real estate that we traditionally placed just the 96.96 genotyping IFC … including all of the corresponding plumbing for the new chambers, and also creating a workflow that allows customers to complete the entire reaction in 2.5 hours," said High of the development process.

"Of course, we also did some great engineering work to get the data reliability and consistency that production genomics customers have come to expect from Fluidigm genotyping," he added.

And Fluidigm's production genomics customers are diverse. High first mentioned clinical labs as a target group, because they will now be able to genotype sample types, such as FFPE and buccal swabs, that typically yield low concentrations of DNA.

"This opens up the types of samples they can accept into their lab," said High.

"Additionally, the integration of preamplification and genotyping on a single IFC will allow clinical labs to genotype with the least amount of hands-on steps of any genotyping platform, which reduces the chances of error," he said.

Another target is biorepositories and cell culture facilities that can use Juno to prepare samples prior to genotyping for identification, quality control, and DNA fingerprinting. "Combined with our SNPtrace Panel, the system is a turnkey solution for this application," said High.

SNPtrace, launched earlier this year, is a panel of 96 SNPs designed to assess the identity and quality of DNA samples.

Fluidigm also intends to sell Juno to agbio researchers and companies. High named seed breeders and wildlife management operations as potential clients for the system. The company similarly sees core labs and service providers as target customers.

"Core labs must accommodate the needs of many different customers," said High. "The system's ability to use variable sample amounts, use different assay types, control and thermal cycle our whole line up of genotyping and digital PCR IFCs ... makes this and the BioMark HD System a perfect all-in-one solution for core labs, instead of having to purchase and support a multitude of different platforms," he said.